Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

A ChIP-Seq Data Analysis Pipeline Based on Bioconductor Packages.

Seung-Jin Park1,2, Jong-Hwan Kim1,2, Byung-Ha Yoon1,2

  • 1Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea.

Genomics & Informatics
|April 19, 2017
PubMed
Summary

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Chondroprotective Effects of Enzyme-Treated Extract from <i>Cervus elaphus</i> L. in a Rat Model of Osteoarthritis.

International journal of molecular sciences·2026
Same author

Integrated multi-omics analysis reveals apple mango leaf extract-induced dendritic cell maturation associated with Il1b upregulation and PU.1/ETS motif enrichment.

Scientific reports·2026
Same author

Thyroid cancer-associated EZH1 Q571R mutation drives chromatin compaction and H3K27me3 invasion into active chromatin.

Molecular cell·2026
Same author

Corrigendum to "Integrative multi-scale physiological, metabolic, and proteomic reprogramming in tomato under polyethylene microplastic stress" [Ecotoxicol. Environ. Saf. 316 (2026), 120148].

Ecotoxicology and environmental safety·2026
Same author

Immune phenotype-based stratification of colorectal cancer reveals subtype-specific immunotherapeutic opportunities: insights from a Korean patient cohort.

BMB reports·2026
Same author

Physical disorders and neuroendocrine vulnerability in the development of posttraumatic stress disorder: A 2-year injury cohort study.

Psychoneuroendocrinology·2026

This study presents a streamlined chromatin immunoprecipitation-sequencing (ChIP-Seq) data analysis workflow using four Bioconductor packages. The workflow efficiently processes sequencing data for DNA-protein interaction studies across all operating systems.

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Vast amounts of chromatin immunoprecipitation-sequencing (ChIP-Seq) data are generated to understand DNA-protein interactions.
  • Numerous computational tools exist for ChIP-Seq data analysis, necessitating efficient and integrated solutions.

Purpose of the Study:

  • To present a streamlined and integrated workflow for ChIP-Seq data analysis.
  • To demonstrate the utility of combining dada2, QuasR, mosaics, and ChIPseeker packages for comprehensive ChIP-Seq analysis.

Main Methods:

  • Utilized dada2 for high-throughput sequencing data trimming.
  • Employed QuasR for quality control and read mapping to the reference genome.
  • Applied mosaics for peak calling and ChIPseeker for peak annotation and visualization.
Keywords:
chromatin immunoprecipitationdata analysisnext-generation sequencingstatistical

Related Experiment Videos

  • Integrated these four Bioconductor packages into a single, efficient workflow.

    • Main Results:

    • The workflow successfully processes raw fastq files into annotated peaks in a single run.
    • The presented ChIP-Seq analysis workflow is compatible with multiple operating systems (Windows, Mac, Linux).
    • The R code for the workflow is publicly available on GitHub.

    Conclusions:

    • This integrated workflow offers an efficient and user-friendly approach to ChIP-Seq data analysis.
    • The streamlined process facilitates the study of DNA-protein interactions from raw sequencing data to biological insights.
    • The workflow's cross-platform compatibility enhances its accessibility for researchers worldwide.